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At least 577 records · Page 32

Plant vacuole morphology and vacuolar trafficking

Plant vacuoles are essential organelles for plant growth and development, and have multiple functions. Vacuoles are highly dynamic and pleiomorphic, and their size varies depending on the cell type and growth conditions. Vacuoles compartmentalize different cellular components such as proteins, sugars, ions and other secondary metabolites and play critical roles in plants response to different biotic/abiotic signaling pathways. In this review, we will summarize the patterns of changes in vacuole morphology in certain cell types, our understanding of the mechanisms of plant vacuole biogenesis, and the role of SNAREs and Rab GTPases in vacuolar trafficking.

chemical biology↗

Arboreal Epiphytes in the Soil-Atmosphere Interface: How Often Are the Biggest “Buckets” in the Canopy Empty?

Arboreal epiphytes (plants residing in forest canopies) are present across all major climate zones and play important roles in forest biogeochemistry. The substantial water storage capacity per unit area of the epiphyte “bucket” is a key attribute underlying their capability to influence forest hydrological processes and their related mass and energy flows. It is commonly assumed that the epiphyte bucket remains saturated, or near-saturated, most of the time; thus, epiphytes (particularly vascular epiphytes) can store little precipitation, limiting their impact on the forest canopy water budget. We present evidence that contradicts this common assumption from (i) an examination of past research; (ii) new datasets on vascular epiphyte and epi-soil water relations at a tropical montane cloud forest (Monteverde, Costa Rica); and (iii) a global evaluation of non-vascular epiphyte saturation state using a process-based vegetation model, LiBry. All analyses found that the external and internal water storage capacity of epiphyte communities is highly dynamic and frequently available to intercept precipitation. Globally, non-vascular epiphytes spend <20% of their time near saturation and regionally, including the humid tropics, model results found that non-vascular epiphytes spend ~1/3 of their time in the dry state (0–10% of water storage capacity). Even data from Costa Rican cloud forest sites found the epiphyte community was saturated only 1/3 of the time and that internal leaf water storage was temporally dynamic enough to aid in precipitation interception. Analysis of the epi-soils associated with epiphytes further revealed the extent to which the epiphyte bucket emptied—as even the canopy soils were often <50% saturated (29–53% of all days observed). Results clearly show that the epiphyte bucket is more dynamic than currently assumed, meriting further research on epiphyte roles in precipitation interception, redistribution to the surface and chemical composition of “net” precipitation waters reaching the surface.

Hargis, Hailey↗

What’s in My Toolkit? A Review of Technologies for Assessing Changes in Habitats Caused by Marine Energy Development

Marine energy devices are installed in highly dynamic environments and have the potential to affect the benthic and pelagic habitats around them. Regulatory bodies often require baseline characterization and/or post-installation monitoring to determine whether changes in these habitats are being observed. However, a great diversity of technologies is available for surveying and sampling marine habitats, and selecting the most suitable instrument to identify and measure changes in habitats at marine energy sites can become a daunting task. We conducted a thorough review of journal articles, survey reports, and grey literature to extract information about the technologies used, the data collection and processing methods, and the performance and effectiveness of these instruments. We examined documents related to marine energy development, offshore wind farms, oil and gas offshore sites, and other marine industries around the world over the last 20 years. A total of 120 different technologies were identified across six main habitat categories: seafloor, sediment, infauna, epifauna, pelagic, and biofouling. The technologies were organized into 12 broad technology classes: acoustic, corer, dredge, grab, hook and line, net and trawl, plate, remote sensing, scrape samples, trap, visual, and others. Visual was the most common and the most diverse technology class, with applications across all six habitat categories. Technologies and sampling methods that are designed for working efficiently in energetic environments have greater success at marine energy sites. In addition, sampling designs and statistical analyses should be carefully thought through to identify differences in faunal assemblages and spatiotemporal changes in habitats.

16 TIDAL AND WAVE POWER↗

Secondary Ion Mass Spectral Imaging of Metals and Alloys

Secondary Ion Mass Spectrometry (SIMS) is an outstanding technique for Mass Spectral Imaging (MSI) due to its notable advantages, including high sensitivity, selectivity, and high dynamic range. As a result, SIMS has been employed across many domains of science. In this review, we provide an in-depth overview of the fundamental principles underlying SIMS, followed by an account of the recent development of SIMS instruments. The review encompasses various applications of specific SIMS instruments, notably static SIMS with time-of-flight SIMS (ToF-SIMS) as a widely used platform and dynamic SIMS with Nano SIMS and large geometry SIMS as successful instruments. We particularly focus on SIMS utility in microanalysis and imaging of metals and alloys as materials of interest. Additionally, we discuss the challenges in big SIMS data analysis and give examples of machine leaning (ML) and Artificial Intelligence (AI) for effective MSI data analysis. Finally, we recommend the outlook of SIMS development. It is anticipated that in situ and operando SIMS has the potential to significantly enhance the investigation of metals and alloys by enabling real-time examinations of material surfaces and interfaces during dynamic transformations.

36 MATERIALS SCIENCE↗

Isolation of Histone from Sorghum Leaf Tissue for Top Down Mass Spectrometry Profiling of Potential Epigenetic Markers

Histones belong to a family of highly conserved proteins in eukaryotes. They pack DNA into nucleosomes as functional units of chromatin. Post-translational modifications (PTMs) of histones, which are highly dynamic and can be added or removed by enzymes, play critical roles in regulating gene expression. In plants, epigenetic factors including histone PTMs are related to their adaptive responses to the environment. Understanding the molecular mechanisms of epigenetic control can bring unprecedented opportunities for engineering solutions to increase the resilience of crops to climate change. Herein, we describe a protocol to isolate the nuclei and purify histones from sorghum leaf tissue. The extracted histones can be analyzed as their intact forms by top-down mass spectrometry (MS) coupled to online reversed-phase (RP) liquid chromatography (LC). Combinations and stoichiometry of multiple PTMs on the same histone proteoform can be readily identified. In addition, histone tail clipping can be detected using the top-down LC-MS workflow thus yielding the global PTM profile of core histones (H4, H2A, H2B, H3). By comparing the PTM profile among samples corresponding to different conditions (e.g. drought vs. control), potential epigenetic marks can be discovered as targets for further characterization using approaches such as chromatin immunoprecipitation – sequencing (ChIP-seq).

59 BASIC BIOLOGICAL SCIENCES↗

PATTERNS OF ACTIVITY IN A GLOBAL MODEL OF A SOLAR ACTIVE REGION

In this work we investigate the global activity patterns predicted from a model active region heated by distributions of nanoflares that have a range of frequencies. What differs is the average frequency of the distributions. The activity patterns are manifested in time lag maps of narrow-band instrument channel pairs. We combine hydrodynamic and forward modeling codes with a magnetic field extrapolation to create a model active region and apply the time lag method to synthetic observations. Our aim is not to reproduce a particular set of observations in detail, but to recover some typical properties and patterns observed in active regions. Our key findings are the following. (1) Cooling dominates the time lag signature and the time lags between the channel pairs are generally consistent with observed values. (2) Shorter coronal loops in the core cool more quickly than longer loops at the periphery. (3) All channel pairs show zero time lag when the line of sight passes through coronal loop footpoints. (4) There is strong evidence that plasma must be re-energized on a timescale comparable to the cooling timescale to reproduce the observed coronal activity, but it is likely that a relatively broad spectrum of heating frequencies are operating across active regions. (5) Due to their highly dynamic nature, we find nanoflare trains produce zero time lags along entire flux tubes in our model active region that are seen between the same channel pairs in observed active regions.

79 ASTRONOMY AND ASTROPHYSICS↗

FORMATION AND PLASMA CIRCULATION OF SOLAR PROMINENCES

Solar prominences are long-lived cool and dense plasma curtains in the hot and rarefied outer solar atmosphere or corona. The physical mechanism responsible for their formation and especially for their internal plasma circulation has been uncertain for decades. The observed ubiquitous downflows in quiescent prominences are difficult to interpret because plasma with high conductivity seems to move across horizontal magnetic field lines. Here we present three-dimensional numerical simulations of prominence formation and evolution in an elongated magnetic flux rope as a result of in situ plasma condensations fueled by continuous plasma evaporation from the solar chromosphere. The prominence is born and maintained in a fragmented, highly dynamic state with continuous reappearance of multiple blobs and thread structures that move mainly downward, dragging along mass-loaded field lines. The circulation of prominence plasma is characterized by the dynamic balance between the drainage of prominence plasma back to the chromosphere and the formation of prominence plasma via continuous condensation. Plasma evaporates from the chromosphere, condenses into the prominence in the corona, and drains back to the chromosphere, establishing a stable chromosphere–corona plasma cycle. Synthetic images of the modeled prominence with the Solar Dynamics Observatory Atmospheric Imaging Assembly closely resemble actual observations, with many dynamical threads underlying an elliptical coronal cavity.

79 ASTRONOMY AND ASTROPHYSICS↗

Radiation-driven outflows from and radiative support in dusty tori of active galactic nuclei

Substantial evidence points to dusty, geometrically thick tori obscuring the central engines of active galactic nuclei (AGNs), but so far no mechanism satisfactorily explains why cool dust in the torus remains in a puffy geometry. Near-Eddington infrared (IR) and ultraviolet (UV) luminosities coupled with high dust opacities at these frequencies suggest that radiation pressure on dust can play a significant role in shaping the torus. To explore the possible effects of radiation pressure, we perform three-dimensional radiative hydrodynamics simulations of an initially smooth torus. Our code solves the hydrodynamics equations, the time-dependent multi–angle group IR radiative transfer (RT) equation, and the time-independent UV RT equation. We find a highly dynamic situation. IR radiation is anisotropic, leaving primarily through the central hole. The torus inner surface exhibits a break in axisymmetry under the influence of radiation and differential rotation; clumping follows. In addition, UV radiation pressure on dust launches a strong wind along the inner surface; when scaled to realistic AGN parameters, this outflow travels at ∼5000 (M/10{sup 7}M{sub ⊙}){sup 1/4} [L{sub UV}/(0.1L{sub E})]{sup 1/4} km s{sup −1} and carries ∼0.1 (M/10{sup 7}M{sub ⊙}){sup 3/4} [L{sub UV}/(0.1L{sub E})]{sup 3/4} M {sub ⊙} yr{sup −1}, where M, L{sub UV}, and L{sub E} are the mass, UV luminosity, and Eddington luminosity of the central object respectively.

79 ASTRONOMY AND ASTROPHYSICS↗

A deep X-ray view of the bare AGN Ark 120. II. Evidence for Fe K emission transients

We report on the results from a large observational campaign on the bare Seyfert galaxy Ark 120, jointly carried out in 2014 with XMM-Newton, Chandra, and NuSTAR. The fortunate line of sight to this source, devoid of any significant absorbing material, provides an incomparably clean view to the nuclear regions of an active galaxy. Here we focus on the analysis of the iron fluorescence features, which form a composite emission pattern in the 6–7 keV band. The prominent Kα line from neutral iron at 6.4 keV is resolved in the Chandra High-Energy Transmission Grating spectrum to a full-width at half maximum of 4700{sub −1500}{sup +2700} km s{sup −1}, consistent with an origin from the optical broad-line region. Excess components are detected on both sides of the narrow Kα line: the red one (6.0–6.3 keV) clearly varies in strength in about one year, and hints at the presence of a broad, mildly asymmetric line from the accretion disk; the blue one (6.5–7.0 keV), instead, is likely a blend of different contributions, and appears to be constant when integrated over long enough exposures. However, the Fe K excess emission map computed over the 7.5 days of the XMM-Newton monitoring shows that both the red and blue features are actually highly variable on timescales of ∼10–15 hr, suggesting that they might arise from short-lived hotspots on the disk surface, located within a few tens of gravitational radii from the central supermassive black hole and possibly illuminated by magnetic reconnection events. Any alternative explanation would still require a highly dynamic, inhomogeneous disk/coronal system, involving clumpiness and/or instability.

79 ASTRONOMY AND ASTROPHYSICS↗

The Pointing Self-calibration Algorithm for Aperture Synthesis Radio Telescopes

This paper is concerned with algorithms for calibration of direction-dependent effects (DDE) in aperture synthesis radio telescopes (ASRT). After correction of direction-independent effects (DIE) using self-calibration, imaging performance can be limited by the imprecise knowledge of the forward gain of the elements in the array. In general, the forward gain pattern is directionally dependent and varies with time due to a number of reasons. Some factors, such as rotation of the primary beam with Parallactic Angle for Azimuth–Elevation mount antennas are known a priori. Some, such as antenna pointing errors and structural deformation/projection effects for aperture-array elements cannot be measured a priori. Thus, in addition to algorithms to correct for DD effects known a priori, algorithms to solve for DD gains are required for high dynamic range imaging. Here, we discuss a mathematical framework for antenna-based DDE calibration algorithms and show that this framework leads to computationally efficient optimal algorithms that scale well in a parallel computing environment. As an example of an antenna-based DD calibration algorithm, we demonstrate the Pointing SelfCal (PSC) algorithm to solve for the antenna pointing errors. Our analysis show that the sensitivity of modern ASRT is sufficient to solve for antenna pointing errors and other DD effects. We also discuss the use of the PSC algorithm in real-time calibration systems and extensions for antenna Shape SelfCal algorithm for real-time tracking and corrections for pointing offsets and changes in antenna shape.

79 ASTRONOMY AND ASTROPHYSICS↗

Resolved Imaging of the AR Puppis Circumbinary Disk

Circumbinary disks are common around post-asymptotic giant branch (post-AGB) stars with a stellar companion on orbital timescales of a few 100 to few 1000 days. The presence of a disk is usually inferred from the system’s spectral energy distribution and confirmed, for a sub-sample, by interferometric observations. We used the Spectro-Polarimetric High-contrast Exoplanet REsearch (SPHERE) instrument on the Very Large Telescope to obtain extreme adaptive optics assisted scattered light images of the post-AGB binary system AR Puppis. Data have been obtained in the V, I, and H bands. Our observations have produced the first resolved images of AR Puppis’s circumbinary disk and confirm its edge-on orientation. In our high-angular-resolution and high-dynamic-range images we identify several structural components such as a dark mid-plane, the disk surface, and arc-like features. We discuss the nature of these components and use complementary photometric monitoring to relate them to the orbital phase of the binary system. Because the star is completely obscured by the disk at visible wavelengths, we conclude that the long-term photometric variability of the system must be caused by variable scattering, not extinction, of starlight by the disk over the binary orbit. Finally, we discuss how the short disk lifetimes and fast evolution of the host stars compared to the ages at which protoplanetary disks are typically observed make systems like AR Puppis valuable extreme laboratories to study circumstellar disk evolution and constrain the timescale of dust grain growth during the planet formation process.

79 ASTRONOMY AND ASTROPHYSICS↗

High-resolution CARMA Observation of Molecular Gas in the North America and Pelican Nebulae

In this paper, we present the first results from a CARMA high-resolution {sup 12}CO(1-0), {sup 13}CO(1-0), and C{sup 18}O(1-0) molecular line survey of the North America and Pelican (NAP) Nebulae. CARMA observations have been combined with single-dish data from the Purple Mountain 13.7 m telescope, to add short spacings and to produce high-dynamic-range images. We find that the molecular gas is predominantly shaped by the W80 H ii bubble, driven by an O star. Several bright rims noted in the observation are probably remnant molecular clouds, heated and stripped by the massive star. Matching these rims in molecular lines and optical images, we construct a model of the three-dimensional structure of the NAP complex. Two groups of molecular clumps/filaments are on the near side of the bubble: one is being pushed toward us, whereas the other is moving toward the bubble. Another group is on the far side of the bubble, and moving away. The young stellar objects in the Gulf region reside in three different clusters, each hosted by a cloud from one of the three molecular clump groups. Although all gas content in the NAP is impacted by feedback from the central O star, some regions show no signs of star formation, while other areas clearly exhibit star formation activity. Additional molecular gas being carved by feedback includes cometary structures in the Pelican Head region, and the boomerang features at the boundary of the Gulf region. The results show that the NAP complex is an ideal place for the study of feedback effects on star formation.

74 ATOMIC AND MOLECULAR PHYSICS↗

Morphological Properties of the Crab Nebula: A Detailed Multiwavelength Study Based on New VLA, HST, Chandra, and XMM-Newton Images

We present a detailed analysis of the morphological properties of the Crab Nebula across the electromagnetic spectrum based on new and previous high-quality data from radio to X-rays. In the radio range we obtained an image of the entire nebula at 3 GHz with subarcsecond angular resolution using the VLA (NRAO) and an image at 100 GHz of the central region using the ALMA array. Simultaneously with the VLA observations we performed HST WFPC3 near-infrared (λ∼1.5 μm) and Chandra X-ray (0.5–8 keV band) observations of the central region of the nebula. In addition we produced a new UV image of the Crab Nebula at 291 nm by co-adding 75 individual exposures of the Optical-UV Monitor on board XMM-Newton. The high-angular resolution and high-dynamic range radio image at 3 GHz allowed us to improve the detection and characterization of peculiar morphological features including arches with foot brightening and intercrossed loop-like structures, likely originating in plasma confined to magnetic field lines. Based on the new radio image, we carried out a detailed multiwavelength correlation. In the central area, the comparison of the almost simultaneous images confirms that the wisps in the three spectral ranges do not generally coincide in location, the radio emission being the most discordant, which is suggestive of the existence of two different synchrotron components. The X-ray pulsar jet does not have a radio counterpart. Instead, another jet-like feature is seen in radio, though with different curvature and starting point.

79 ASTRONOMY AND ASTROPHYSICS↗

A Tale of Two Emergences: Sunrise II Observations of Emergence Sites in a Solar Active Region

In 2013 June, the two scientific instruments on board the second Sunrise mission witnessed, in detail, a small-scale magnetic flux emergence event as part of the birth of an active region. The Imaging Magnetograph Experiment (IMaX) recorded two small (∼5{sup ′′}) emerging flux patches in the polarized filtergrams of a photospheric Fe i spectral line. Meanwhile, the Sunrise Filter Imager (SuFI) captured the highly dynamic chromospheric response to the magnetic fields pushing their way through the lower solar atmosphere. The serendipitous capture of this event offers a closer look at the inner workings of active region emergence sites. In particular, it reveals in meticulous detail how the rising magnetic fields interact with the granulation as they push through the Sun’s surface, dragging photospheric plasma in their upward travel. The plasma that is burdening the rising field slides along the field lines, creating fast downflowing channels at the footpoints. The weight of this material anchors this field to the surface at semi-regular spatial intervals, shaping it in an undulatory fashion. Finally, magnetic reconnection enables the field to release itself from its photospheric anchors, allowing it to continue its voyage up to higher layers. This process releases energy that lights up the arch-filament systems and heats the surrounding chromosphere.

79 ASTRONOMY AND ASTROPHYSICS↗

The Detectability of Radio Auroral Emission from Proxima b

Magnetically active stars possess stellar winds whose interactions with planetary magnetic fields produce radio auroral emission. We examine the detectability of radio auroral emission from Proxima b, the closest known exosolar planet orbiting our nearest neighboring star, Proxima Centauri. Using the radiometric Bode’s law, we estimate the radio flux produced by the interaction of Proxima Centauri’s stellar wind and Proxima b’s magnetosphere for different planetary magnetic field strengths. For plausible planetary masses, Proxima b could produce radio fluxes of 100 mJy or more in a frequency range of 0.02–3 MHz for planetary magnetic field strengths of 0.007–1 G. According to recent MHD models that vary the orbital parameters of the system, this emission is expected to be highly variable. This variability is due to large fluctuations in the size of Proxima b’s magnetosphere as it crosses the equatorial streamer regions of dense stellar wind and high dynamic pressure. Using the MHD model of Garraffo et al. for the variation of the magnetosphere radius during the orbit, we estimate that the observed radio flux can vary nearly by an order of magnitude over the 11.2-day period of Proxima b. The detailed amplitude variation depends on the stellar wind, orbital, and planetary magnetic field parameters. We discuss observing strategies for proposed future space-based observatories to reach frequencies below the ionospheric cutoff (∼10 MHz), which would be required to detect the signal we investigate.

79 ASTRONOMY AND ASTROPHYSICS↗

Heavy-Duty Nonroad Material Handler Electrification Part 2: Energy Efficiency and Performance Evaluation

Decarbonization efforts achieved through electrification in nonroad mobile machinery can realize a reduction in fuel consumption of more than 20%, thanks to concepts familiar to light-duty passenger vehicles. This case study compares the results of a hybrid-electric material handler to its conventional counterpart, utilizing machine-specific drive cycles presented in part one of this paper series. The hybrid prototype features an extended-range electric vehicle (EREV) powertrain that demonstrated substantial energy efficiency improvements. Specifically, there was a reduction in equivalent fuel consumption of 75% when operating in electric-only mode, and 33% when maintaining the battery by charging with an on-board generator. Together, the efficiency improvements can be extrapolated over a low-intensity, 8-h shift characterized by significant idle time and highly dynamic engine load for a 47% reduction in net energy consumption. Key technologies that led to this improvement included engine downsizing and decoupling, regenerative braking, and an electrohydraulic pump unit with advanced controls. Finally, his study explains details of the powertrain architecture and subsystems that were implemented on a demonstration vehicle, control strategies used to meet project goals, and an analysis of energy consumption from testing on a closed course. Also included in this study is a discourse on comparison metrics that can be used for quantifying the energy consumption differences between hybrid-electric and conventional diesel powertrains in nonroad mobile machinery.

25 ENERGY STORAGE↗

Experimental Investigation of Low Cost, Low Thermal Conductivity Thermal Barrier Coating on HCCI Combustion, Efficiency, and Emissions

In-cylinder surface temperature is of heightened importance for Homogeneous Charge Compression Ignition (HCCI) combustion since the combustion mechanism is thermo-kinetically driven. Thermal Barrier Coatings (TBCs) selectively manipulate the in-cylinder surface temperature, providing an avenue for improving thermal and combustion efficiency. A surface temperature swing during combustion/expansion reduces heat transfer losses, leading to more complete combustion and reduced emissions. At the same time, achieving a highly dynamic response sidesteps preheating of charge during intake and eliminates the volumetric efficiency penalty. The magnitude and temporal profile of the dynamic surface temperature swing is affected by the TBC material properties, thickness, morphology, engine speed, and heat flux from the combustion process. This study follows prior work of authors with Yttria Stabilized Zirconia, which systematically engineered coatings for HCCI combustion. Herein, a modeling study was used to assess the impacts of various TBC material properties, e.g. density, thickness, and thermal conductivity on the temperature swing effect. Reducing conductivity emerged as a most promising avenue, rather than reducing both the density and effective conductivity by increasing porosity, the current work emphasizes a material with natively low conductivity. A novel TBC formulation was developed, leverages a class of materials that, to the author’s best knowledge, have not been used as a thermal barrier coating previously. Here, a systematic experimental investigation was carried out using single-cylinder research engine. Experimental engine studies utilizing the novel ‘glassy’ low-K coating exhibit advanced ignition phasing and reduced combustion duration relative to the baseline engine. Heat transfer measurements indicate a net reduction in heat flux over the entire cycle, although main effect is felt during expansion, and the reduced heat transfer losses manifest in higher gross indicated thermal efficiency by approximately 5-6% on a relative basis.

42 ENGINEERING↗

A large accessory protein interactome is rewired across environments

To characterize how protein-protein interaction (PPI) networks change, we quantified the relative PPI abundance of 1.6 million protein pairs in the yeast Saccharomyces cerevisiae across 9 growth conditions, with replication, for a total of 44 million measurements. Our multi-condition screen identified 13,764 pairwise PPIs, a 3-fold increase over PPIs identified in one condition. A few 'immutable' PPIs are present across all conditions, while most 'mutable' PPIs are rarely observed. Immutable PPIs aggregate into highly connected 'core' network modules, with most network remodeling occurring within a loosely connected 'accessory' module. Mutable PPIs are less likely to co-express, co-localize, and be explained by simple mass action kinetics, and more likely to contain proteins with intrinsically disordered regions, implying that environment-dependent association and binding is critical to cellular adaptation. Our results show that protein interactomes are larger than previously thought and contain highly dynamic regions that reorganize to drive or respond to cellular changes.

59 BASIC BIOLOGICAL SCIENCES↗